An additional bug to look into for Warzone pulled out of old posts on the forum:
Pardon the bump, but I'm having one of the same problems Turalyon was with Warzone. I'm at the mission "Stacking the Deck," and I am getting all primary objectives completed, getting my "congratulations and well done" messages at the mission review screen, but I then when I try to "accept" I get a message saying I can't because I failed the mission.
Another weird thing about this mission was that I could choose any weapon and any ship I wanted at the loadout stage. Even an SF Mara. Did this happen with anyone else besides Turalyon?
EDIT:
Bah! Nevermind. I just managed to get through successfully. The original problem was caused by one of two things. 1) It didn't like me using a non-standard loadout (unlikely) or 2) The bonus objective of scanning the Vidar (which I didn't know about until this time around) was actually required for the mission to be considered "successful." Either way, problem solved.